The association of FTO gene variants with body mass index (BMI) and other obesity characteristics is well established. However, uncertainties remain whether the association is present only in young populations and whether it is attributable to body fat mass specifically. We aimed to clarify these two questions in a large sample (N= 4,523 individuals) of middle-aged and older (range 40–80 years) British female twins. The women were assessed for BMI, waist and hip circumference, total lean (LBM) and fat (FBM) body mass. Since the majority of FTO association signals have been reported in a haploblock bordering 52,355–52,408 kb (on chromosome 16q12.2), we examined five genotyped and 43 imputed SNPs mapped to this block. Canonical correlation and other association analyses showed significant and consistent association between the selected SNP and studied body composition phenotypes, with p-values reaching p= 0.000004. Of particular interest, in addition to the expected significant associations between FTO variants and FBM, we also identified significant associations with LBM. These results suggest that the association between FTO variants and body composition phenotypes is present across a wide range of ages, and that FTO appears primarily to affect the amount of body soft tissue, influencing both fat and lean mass.